I've come from an X-T1, I really miss the tilting screen for low shots but other than that I've not experienced anything of major concern.
The main annoyances are that I'm not a fan of the wheel selector thingy, and having to think/worry about micro-adjusting lenses is a real pain having been used to the unnerving out-of-the-box accuracy of mirrorless. On the point of AF, the X-T1 is pretty darn rapid in the AF stakes now, the 6D really doesn't feel that much different.
It's nice that relatively speaking, lenses are so much cheaper and obviously the choice is huge, but saying that you need really good (generally L) glass to match the stunning Fuji efforts. Having reasonably reliable indication of battery life is also a bonus!